Dongshan,
You can either develop your own code, or use someone else's such as:
Alan Grossfields: http://membrane.urmc.rochester.edu/content/wham
or
John Chodera's: http://www.dillgroup.ucsf.edu/~jchodera/code/WHAM/
Someone else might have a "more straightforward" way of doing this.
I use my own code, but in its current condition I couldn't lend it out *yet*in
full conscience. :P
--Dan
On Tue, Jul 27, 2010 at 7:43 AM, Dongshan Wei <dswei0523.gmail.com> wrote:
> Hi Everyone,
>
> Recently I want to do a ramachandran plot for an Alanine peptide. I
> did a 10ns temperature REMD simulations with 16 replicas. Now I want
> to weight the probability for temperatures not at T0 to get the
> weighted ramachandran plot. I made a quick look through the mailing
> list and find most WHAM is combined with umbrella sampling. Can
> somebody give a clear procedure on how to do WHAM based on REMD
> simulations outputs?
>
> Thanks so much!
>
> Dongshan
>
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--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Tue Jul 27 2010 - 04:30:03 PDT
